The nuclear threat
by The Frozen Sock
Summary: Atlantis is derelict. An Ex Spec Ops team has turned terrorist and captured this vital point in the Pegasus Galaxy. X over. MGS & SGA. First *serious* story, please review.
1. Chapter 1

The Briefing

Shepherd lay where he was, trying to remember the briefing that Hammond had given him.

"The derelict Ancient City on LM9-2K2 in the Pegasus Galaxy was attacked and captured by Next - Generation Special forces, being led by members of FOX-HOUND.

Shepherd had been taken in the night from his home in Nebraska. He'd retired from the Forces. Why did Hammond need him now? He just sat on his prison cell's bed, and listened.

"They're demanding the government turn over the remains of Big-Boss, and they say that if their demands aren't met within 24 hours, they'll launch a nuclear weapon."

Now Shepherd started to care. This is what he'd been trained for; and this was why he'd been kidnapped in the middle of the night. He was the only person that was capable of taking on this mission.

"You'll have two mission objectives. First, you're to rescue IOA investigator Richard Woolsey, and the SGC boss, Hank Landry. Both are being held as hostages. Secondly, you're to investigate whether or not the terrorists have the ability to launch a Nuclear strike, and stop them if they do."

He had begun to think this through by that point. The problem was, getting to the city without being detected. "What's the insertion method?" he'd asked.

"We'll leave hyperspace about 3 miles from orbital range, just outside of their long-range radar."

"And then?" Shepherd asked, wondering how _he_ was going to get in.

"We'll launch a one-man SDV. once you get into the atmosphere, dispose of it. From there on you'll have to freefall into the city's bay."

"Anyone going with me?" Shepherd had said, sounding hopeful.

"As usual, this is a one man infiltration mission. Weapons and equipment, procured on-site. Don't expect any official support."

And so Shepherd continued to rehearse the briefing, over and over in his head, while he lay in his SDV. It was a small, torpedo shaped deployment vehicle designed for use in water, and in space. It would get him through the atmosphere, at least.

He felt violent jerks as the SDV shot out of the Daedalus at high speed. He could see the planet coming closer through the small window in front of his face.

The window turned red as it hit the atmosphere, plunging the ship even further and faster as the gravity took effect.

The flames turned to smoke as it broke through, Shepherd keeping his eye on the altimeter - he was waiting for the 20,000 feet marker.

He shot right past it - now it was safe for the planned HALO jump. He punched a button to his left, splitting the SDV in half while he dodged the parts and began to freefall.

He couldn't open his parachute until he was close enough... if he pulled the cord too early, the terrorists would spot him and the mission would be over before it had begun.

He streamlined himself to fall even faster. He began to sweat violently under his helmet, but kept his eyes open. 15,000 feet.

The clouds cleared, and he saw Atlantis. Since the expeditionary team left it had been completely derelict. Everyone had gone their seperate ways. 10,000 feet.

Shepherd had joined FOX-HOUND, along with Ronan and Carter. He had retired. That was before FOX-HOUND turned to terrorism... they must be hoping to establish a base at Atlantis at which to launch an effective strike against Earth.

Shepherd wondered if Ronan and Carter had anything to do with this... and Big Boss, the leader... well, he could hardly believe O'neill formed the group. 5,000 feet.

He began to slow himself down as the water sped towards him. he looked to his left as the control tower in the city some distance away began to rise above him. He pulled the cord and looked for a bay to the ocean he could land in as the parachute rose above him like a shield and slowed him down tremendously.

He landed on a dock and after detaching his parachute, hid it in a disused cargo box. He hid himself from sight by running into the underground Dock. He switched on his radio. "Hammond, I'm in."


	2. Infiltration

Infiltration

"Shepherd, this is no ordinary mission. After Landry was taken as a hostage I was immediately reinstated as head of the SGC. I'm here as your official CO, but there's nothing we can do from this distance besides give you information via your radio."

Shepherd took a look around the inside of the dock from his hiding place behind a crate. "There's nobody here. Looks like their numbers aren't too large - otherwise they'd be crawling all over the city." He stood up and made a short burst for the lift at the back of the room.

"Don't let your guard down - just because they're not _everywhere _doesn't mean they won't have a unit in that area." Shepherd looked up the shaft from the cargo lift - _this must go hundreds of feet up... _he pressed the "up" button and the lift steadily rose. _you've gotta be kidding me..._

"Shepherd, they're suspecting a hostile presence in the city. The remains of your SDV were found - we managed to modify the shell to make it look like a drone incase this happened, but we _have _to send down puddle jumpers and make it look like we're launching an offensive before they suspect you've actually arrived."

"I'm that important huh?" Shepherd said with a wide grin on his face. The lift sped up, and he soon arrived at the top floor. "I'm in - moving outside to get a clear view of the city," he said.

Shepherd took the stairs to the roof and dove behind a giant crate as he noticed an armed guard patrolling the roof. He leant right a bit to see where he was.

"Colonel, you won't believe this... They have a 302 on the roof... how the hell did they get their hands on it?" he whispered. He felt like his luck had just ran out.

"Fox-Hound wasn't just an infantry regiment. They were deemed important enough for their own personal Fighter Support. I suspected they'd have one..."

He looked around for signs of a pilot - and sure enough, someone walked out wearing the complete gear. _I know who that is...! _but he only had a guess, as the man put the helmet on and climbed into the cockpit.

"Colonel, they're taking off - your Jumpers will have a fight on their hands, it looks like you caught their attention." as the 302 rocketed into the sky, the armed guard moved downstairs through the doorway Shepherd had been stood in.

He got up and moved to the edge of the tower he was stood on. "I'm in the outskirts here. I have to make my way across the the main tower, but there's no walkway," he said.

"The schematics of the city show a walkway about ten storeys below you. You should fast rope down, it's the easiest way."

Shepherd looked down, and sure enough, there it was, far below him. He attached his hook to the crate he had hidden behind, threw his rope over the edge and threw himself off the roof. He shot downwards, and hit the walkway with enough force to cripple him.

"Always hate those landings... right, I'm off to the prison block, see if I can locate Landry or Woolsey. I'll keep you posted."


	3. Realisation

Realisation

Shepherd took a look around at the surrounding buildings of the city. He had some good cover here from Atlantis' Control Tower so he was in no immediate danger. He took a few steps forward before he heard a sickening crack above his head.

the 302 had just shot the first Puddle Jumper to pieces right over him - on fire, it began to fall, the roar of engines soon caught up with him, as the Puddle Jumper exploded on impact against the Tower behind him. Shepherd made a desperate dash for the far end of the walkway.

The second Puddle Jumper shot like a bullet under the walkway, closely followed by the 302 - _damn, that's one good pilot... _They darted between buildings in a furious game of cat and mouse before they shot out of the streets into the sky - the 302 unleashed a flurry of bullets and the second Jumper blew into a million pieces.

"Colonel! that 302 just took out two Puddle Jumpers... he has some real skill if he can pull that off without the help of the Ancient Gene! it's practically impossible to take down a Jumper, it has all the advantages!"

"We know... and the Daedalus isn't happy about its loss at all. Make this mission worth it, Shepherd, we just lost two good pilots down there. Find out who that pilot _is, _shepherd." said Hammond sounding _very_ frustrated.

The 302 flew back over his head and shot towards the other side of the city, doing a Victory Roll in the process. _show off..._ Shepherd moved into the building he'd been taking shelter at. There were lockers on every wall, a lift in the centre of the room, and a door at the far end.

He took cover behind a crate as he heard voices moving closer. "So, what the hell did you need to talk to me about? the next time you run at me and pull me out of my patrol, you're getting shot," said the first of the guards, who came through the opposing door with somebody else. He took time to look at the panicking man who'd pulled him down the hallway... "You're sweating... you look like you've seen a ghost," he said.

"Listen, there's some_thing_ on this base - not one of our own," said the second. _something? that can't be me..._

"What? why didn't you report it to the CO!?" the first one shouted, getting frustrated.

"The intruder... he's not human... he cu-ut down m-my squad on a routine p-patrol through the medical qua-arter... He's using some kind of s-sword!" the second man stuttered.

"Snap out of it you daft prick, nobody else has seen this 'intruder,' you're probably just high, I told you to stop taking that E..." said the first, entirely unconvinced.

"Of course you didn't see him! he's using Jumper technology, you can't even -" just as the second man was getting somewhere, their radio crackled.

"Alpha Squad, fall back to the Control Tower, somebody wiped out an entire Patrol, we have an intruder, and I want to know who it is!" the man shouted over the radio, and the two guards looked at eachother.

"Now I think I believe you. Let's get back to the Tower and tell them what you saw," said the first man, as they both ran through the door ahead.

_something did that to a patrol? what could it be? _thought shepherd. "Colonel, there's an intruder on the base besides me. He's cut down an entire patrol, and nobody has a damn clue where it is," said shepherd over his radio.

"Well you did get some kind of 'support' at least... just... take advantage of the work and find the hostages. The building you're in should have a prison block a few floors down, the Hostages should be there. There are 15 hours left until their deadline, Shepherd. We need that nuke ID'd and disposed of before then." hammond said.

Shepherd looked around - this looked like some kind of armoury... he walked over to a locker at the far end of the room and kicked it open. There was a Beretta 92fs sat on a shelf with a locked slide. He picked up the boxes of ammo near it and dropped them in his chest pouches. He slided a magazine into the 92fs, and the slide shot back into place.

He got in the lift at the centre of the room, holstering his newfound weapon. the little flashing light kept decreasing until one of the little Ancient lights lit up and the doors opened.

"Shepherd, we're reading Woolsey's signal in the room to your left - hurry in there and get him out for extraction," the colonel's voice came over his radio.

Shepherd ran down the hallway and took a left turn - there was a door into the room on his left. He entered, and flinched as he saw a guard - before noticing he was snoring loudly on his chair. Shepherd grabbed the cell's keys from the desk and unlocked the door on the farthest left.

Woolsey looked like he'd been tortured for information... but Shepherd shut the door behind him so he couldn't get out.

"Shepherd!? what are you doing here!?" woolsey said, scanning him up and down.

"I'm the pawn they sent in here to save your ass, but I want information first," Shepherd said.

"Anything you want to know, just get me out of here!" Woolsey looked desperate now.

"Hold on. We need to know - do the terrorists really have the ability to launch a nuclear strike?" Shepherd asked without blinking. He'd come here for this, so he should make it worth it.

"Why? what are they doing?" Woolsey said, looking confused.

"Fox-Hound are threatening the US, and they say that if their demands aren't met in the next 15 hours, they'll launch a nuclear weapon,"

Woolsey looked shocked. "What are their demands?" he asked.

"The remains of O'Neill. And one billion dollars." Shepherd felt like this was coming from the mouth of a terrorist itself...

Woolsey almost fainted. "They can't ask for that much!" he said, falling back onto his bed. "Ok... so they _could_ launch a Nuke..."

"What!? this is a derelict city with no real source of power, where'd they get a Nuke from!?" Shepherd shouted.

"It was here all along. When the Atlantis expedition failed, the Government decided to put the base to some use, and stored a few Warheads here..."

"Those idiots! they were too vulnerable!" Shepherd gasped.

"And they found out my password! I never could resist torture..." Woolsey began to moan.

"Your password?" Shepherd asked, confused.

"Yes. My password. I know one, and Landry knows one. Both of our passwords are needed to disengage the safety device. Only then can you make a Nuclear Strike," Woolsey sobbed.

"You've said enough - Get to the roof and I'll call for a cloaked puddle jumper as your extraction. I'm gonna go get Landry," Shepherd said.

"Shepherd... thanks for doing this - it means a lot... I never - wait, do you hear that?" Woolsey whispered.

The sound of a fight going on outside met their ears. There was loud shout, a deafening crack as somebody fell to the floor, and after a few minutes, the door opened...


	4. Realisation, Part 2

Realisation - Part 2

_(AN: sorry about the late update. Bad internet connection and Work Experience do these things, you know. :) ah yes, and my sister also pointed out I'd been spelling "sheppard" wrong for the last few chapters. So... that's like fixed now... :P )_

Sheppard whipped up his Beretta and aimed out of the doorway - nobody there. he made a notion to Woolsey telling him to keep quiet - he nodded, and Sheppard moved up to the doorway. He tilted his head, and saw an unconcious guard outside. He moved out and -

"Sheppard!?" came a voice to his left - he turned quickly and tightened his grip on the trigger.

"Teyla!? what are you doing here?" Sheppard gasped. The cell next to woolsey's was open - Teyla was right next door! She loosened her grip on her newly aquired L98 assault rifle. Sheppard did the same, lowering his beretta.

"There's no time - we've got to get to a safer place -" she began to stutter. Woolsey ran out of his cell to the prison door.

"Teyla, what are you on about?" Sheppard said.

"Forget it - look out!" she shouted, as the door into the prison opened, and three soldiers entered, gunning Woolsey down where he stood...

"Fox - Hound? damn it!" Sheppard shouted, releasing three bullets into each soldier. They dropped to the floor with a huge thud.

"No! Woolsey! Colonel, come in... Woolsey's dead, he got hit by Fox Hound on exfil! I'm on my way to Landry, we can still get him out!" Sheppard shouted down his radio. He beckoned Teyla to follow him as they moved up to the old hallway to the lift.

"Teyla, what the hell are you doing here?" Sheppard whispered, in case more guardswere around.

"When you left Fox-Hound, Sheppard, I joined to replace you. Only now, when they rebelled against the government and went rogue, I didn't agree with their revolt, and they threw me in here," she returned.

Sheppard's heart pounded. "What then?"

"Ronan and Carter didn't follow with me. They joined... I couldn't believe it..." she said.

They got in the lift and moved down until another one of the strange atlantean lights changed in the lift. Sheppard's heart continued to beat against his chest. Ronan and Carter had joined the _terrorists?_

Sheppard tried not to think about it. "Right, erm, you wait here, I'll find Landry. Then we have to get you and him out of here as soon as possible," he said rhetorically.

Teyla did as she was asked and, kneeling down, watched the opposite end of the corridor through the L98's sights.

Sheppard tried to make sense of what was going on while he walked down the hallway, gun in hand. Fox-Hound had rebelled except Teyla... that was everybody he _knew..._ Ronan, Carter, even Lorne - and he didn't even know about it!

He moved up to a door ahead that slid open as he neared it - inside, strapped to a pillar with ropes coming off to the walls in every direction, was Landry. Sheppard burst into the room - there was no guard.

"Landry, you alright?" he said. Landry didn't open his eyes and his bruised face remained unflinching. "Landry!" he shouted.

Landry woke with a start and flinched at the sight of Sheppard. "Leave! you have to! these ropes... they're strapped to c4..." he said, coughing up blood. Sure enough, as Sheppard looked around, he saw it plastered to the walls, the ceiling, the floor...

A giant red flash hit the floor at Sheppard's feet. Ronan stepped out from behind the pillar. "Right... touch that wire, and the c4 blows up along with the old man..." Ronan directed at him.

Ronan could always beat him in a fight. Sheppard began to sweat. They both had their guns aimed on eachother's heads. "Make your move."


	5. Confusion

Confusion

_(the ronon thing is also fixed... :) )_

Sheppard dove behind one of the four pillars surrounding the central pillar that Landry was roped to - he was careful to avoid the tripwires as he moved. "Ronon! why did you do this? Why did you turn!?" he shouted.

Ronon had remained unmoving, and had followed sheppard's dive with his eyes, not his gun. "They offered me more money, Sheppard! enough to let me retire and stay low for the rest of my life!" he shouted, as he fired a red bolt from his gun at Sheppard's pillar.

Sheppard retorted by firing blindly round the side, forcing Ronon into cover too. "We were brothers, Ronon, best friends - why would _you _give all that up for some money?" Sheppard shouted back.

"You've gone soft, John. I knew you would when you betrayed us and left us without a squad leader..." Ronon said, barely audible.

Sheppard looked around the room - so many trip wires plastered to the walls, holding Landry in place - how was he going to get around to hit Ronon from the side? "Is that so?" he said without really thinking, trying to keep Ronon's mind on the conversation as he glanced around the room even quicker.

"You always were good in a fight, John - but we're not even warmed up!" he shouted as they both jumped around the corners of their pillars, guns pointed at eachother, as the same plan had obviously cropped up in both their heads - and now they were back at square one.

A strange sound met their ears - that of a blade slicing through flesh - and a few seconds later, bringing a look of shock to both their faces - Ronon's arm dropped to the floor, severed at the elbow.

A few seconds went by with both of them staring at the stub with looks of awe on their faces, before it began to gush with blood uncontrollably, sending his arm flying. "What?! My hand!" Ronon shouted, as if only just noticing.

Sheppard looked away - glancing around the room as fast as he could to see what had caused it - and a split second later, the sound met his ears again - but this time, the blade was slicing through - _the tripwires! _he thought, and watched them flick back to their explosives as each wire was cut around the room. Landry fell to the floor as he was no longer being held up, and the explosions sent Ronon and Sheppard flying into opposite walls.

They both got to their feet, Ronon gathering his severed hand off the floor as he got up - and they saw it. Invisible at first, but appearing with a loud Screech, stood a - _well, what is it? _sheppard thought.

A fully armoured cyborg - but in human form? - its plates the colours of dull blue and orange - stood before him, its single orange robotic eye at the centre of the faceplate pinging on as it looked straight at Sheppard.

"Jumper Technology?! can't you even die right!?" Ronon shouted. The cyborg looked right at him, obviously striking fear into him as the blood-soaked blade steadied in his hand.

"You were lucky... We'll meet again!" He shouted at Sheppard, turning and running from the room.

The cyborg looked back at Sheppard. He raised his gun at it, wondering _what the hell it was - _"Who are you!?" he shouted at it.

The Cyborg Ninja's eye pinged black then orange again, as it walked steadily towards him. Sheppard backed away, hitting the wall - he began to sweat, and his gun began to shake. "I'm like you." It said in a deep, robotic, strangely _familiar_ kind of voice. "I have no name."

Sheppard glanced at Landry as he moaned back into existence on the floor. "That... that exoskeleton!" he said, lying there. Sheppard looked at the Cyborg ninja, wondering what the hell he meant. It glanced over to Landry, then back at Sheppard. They eye glowed even brighter, then he disappeared again into invisibility with the same loud screech. Sheppard didn't have a clue where it had gone, but it was no longer there.

"Landry! Landry, are you ok!?" he shouted over, afraid to move from his spot. Deadly silence had filled the room.

Landry groaned a sound as if he was ok, and got to his feet. "Landry, what the hell was that Ninja thing?" he said, forgetting to lower his gun until he noticed himself still holding it up.

"We were here to oversee Atlantis' nuclear armament capability tests," Landry began. Sheppard backed against the wall, and lowered himself to the floor, still not believing what he had seen.

"It was all our fault - SGC put Fox Hound in defence of the base because we thought they would defend it to the last breath. They betrayed us. Fox Hound had their own scientists... Medical research... They weren't just a unit anymore, but they'd grown into what could be a PMC, running itself, and the hostile's takeover was just a matter of time..." he said.

"You mean you knew this could happen?" Sheppard said, half annoyed, half believing him.

"Yes... that's not the best of it, either... We'd received reports that they were doing their own tests - illegal in their own form, against human rights - and from these experiments, That Cyborg was born." Landry told him.

"You mean that _thing _was once human!?" Sheppard said, glancing up at him questioningly.

"Possibly... and it was employed as a defensive measure for Fox Hound to use, but it turned against its creators some time ago, and it's been giving them major problems ever since." Sheppard let his face fall into his hands - this hand been one hell of a day so far.

Teyla came running in, her rifle at the ready. "John! are you ok? what happened?" she said, looking at the scorch marks and shattered pillars around the room in awe.

"Bit of an explosion. No worries, Landry's safe," he said as if this was a throwaway comment. Teyla looked at him.

"John, you're bleeding. are you sure you're alright?" she asked concernedly, lowering her rifle and kneeling down at the side of him.

"After everything so far, I'm surprised that I'm _only _bleeding." he said sarcastically. "Anyways, let's get Landry and... you know... Woolsey to exfil while we can. This place'll be crawling with Fox Hound after the racket we just made," he said, lifting the now slumped Landry onto his shoulder.

"Wait... you can't go yet..." Landry said, slightly cringing.

"Why? what's wrong?" Sheppard said, moving to the doorway, looking out of it and glancing both ways.

"The terrorists... they know my password..." He said weakly.

Sheppard's senses felt like they'd just got ten times sharper. "What!? you talked!?" he shouted, looking at the side of Landry's face, Teyla's sounds of confusion behind them.

"I never could resist torture... was never very good at it..." he said, even quieter now. "A lot of my bones are shattered, John. I'm not making it out of here." Landry said, his words hitting him and Teyla like bricks.

"Well, I didn't think you would anyway," Said Sheppard, sounding as if he was giving up. Teyla gasped behind him, but Landry just laughed - Sheppard put him down and sat him up by the wall.

"I haven't told you about the nukes... they're not on their own..." he said, his voice failing drastically now.

"Wait, what do you mean? how are they not on their own?" he asked, desperately needing answers.

"The government funded one last thing... A tank... Not just any tank - a bipedal one. Capable of launching a nuclear strike from anywhere on earth... they called it... Metal Gear." He said, before his head dropped to one said, his face expressionless, his eyes open. Teyla began to cry. Sheppard just closed his eyes. This was _really _going to be a lousy day.


End file.
